I assume by now that you've read Interview Magazine's much talked about interview with Joaquin Phoenix in which he hates on the utter bullshit of awards season?
A lot of people have already (and might continue to) lost their minds over this but Serious (Male) Thespians are allowed to get away with trashing the prize they're in the running for. See also: Marlon Brando, George C Scott and others throughout entertainment history. It's the actresses and the less Serious Thespians that have to tread carefully and bat their eyelashes at voters, play a smart hand and shake the right ones, and kiss the babies. The only time this other group (i.e. the less acclaimed talents or the actors with vaginas) can refuse to play the game and still be awarded for it is if they've garnered an unassailable legendary reputation (think Katharine Hepburn who, like Woody Allen, couldn't be bothered to attend her Oscar ceremonies) or delivered work so seismic that voters wouldn't have been able to ignore it and still feel even remotely like they've ever once contemplated the word "Best" in any real way (think Mo'Nique in Precious)
The only reason to worry about Phoenix's nomination chances are the depth of the leading actor field, not his personal statements.